Over the last years, the entire genomes of human and many other model organisms have been sequenced. In many of these organisms, sequencing of the entire genomes has been finished already. There has also been ongoing development in the analysis of transcripts and proteins based on the sequence information of genomes. Specifically, transcriptome analysis and proteome analysis have won the recognition. The transcriptome analysis is used for the analysis of transcripts, whereby the expression of all transcripts in an organism or cells are analyzed both systematically and comprehensively. The proteome analysis is a systematic and comprehensive method of analyzing proteins, in which the properties or expression of all proteins expressed at any given location and any given time in an organism or cells are analyzed.
For the systematic and comprehensive analyses, various array techniques are often used. The array technique refers to a technique using an array, in which biosubstances, such as DNA or various proteins obtained from the organism of interest being analyzed, or synthetic substances (for example, compounds with hydrophobic groups or ion exchange groups) that interact with such biosubstances are immobilized on a support in an orderly manner.
With the array technique, the systematic and comprehensive analysis can be performed efficiently. For example, for the analysis of gene transcription control mechanism, it is required to measure transcription level of genes, which varies according to the state of the cell. For this purpose, use of a DNA micro array, one form of the array technique, allows for systematic measurement of transcription level of several thousand to several ten thousand of genes. Among such DNA micro array techniques, one that has been widely used is the DNA micro array technique developed by Affymetrix. In this technique, oligonucleotides are directly synthesized on a silica substrate using a microfabrication technique employed in the fabrication of semiconductors (see Patent Document 1, for example). Meanwhile, arrays have been developed that are modified to detect single nucleotide polymorphism (SNP) (see Non-Patent Documents 1 and 2, for example).
In order to reduce breeding time, labor, and field area, breeding of Triticeae species nowadays employs a method whereby screening is made using genetic markers as an index. Genetic markers have been used since the advent of DNA markers in the late 1980s, and the study of linkage map has advanced greatly with the use of DNA markers. Today, linkage analysis is performed in many organisms based on their high-density linkage maps. Currently, genetic markers that are strongly linked to target traits are available. By using these genetic markers, breeding can be performed more efficiently. The inventors of the present invention have been actively developing genetic markers in Triticeae species. For example, the inventors have proposed (1) a technique concerning genetic markers that are linked to genes conferring aluminum resistance to barley, and use of such genetic markers (see Patent Publication 2), and (2) a technique concerning novel primer sets that are used to detect barley chromosome nucleic acid markers on a wheat background (see Patent Publication 3), and use of such primer sets.
[Patent Publication 1]
Japanese Laid-Open Patent Publication No. 2000-228999 (published on Aug. 22, 2000)
[Patent Publication 2]
Japanese Laid-Open Patent Publication No. 2002-291474 (published on Oct. 8, 2002)
[Patent Publication 3]
Japanese Laid-Open Patent Publication No. 2003-111593 (published on Apr. 15, 2003)
[Non-Patent Publication 1]
Jobs M, Howell W M, Stromqvist L, Mayr T, Brookes A J. Related Articles, Links. DASH-2: flexible, low-cost, and high-throughput SNP genotyping by dynamic allele-specific hybridization on membrane arrays. Genome Res. 2003 May; 13(5): 916-24.
[Non-Patent Publication 2]
Matsuzaki H, Loi H, Dong S, Tsai Y Y, Fang J, Law J, Di X, Liu W M, Yang G, Liu G, Huang J, Kennedy G C, Ryder T B, Marcus G A, Walsh P S, Shriver M D, Puck J M, Jones K W, Mei R. Links. Parallel Genotyping of Over 10,000 SNPs Using a One-Primer Assay on a High-Density Oligonucleotide Array. Genome Res. 2004 March; 14(3): 414-25.
As described above, genomes of many organisms have been sequenced and many type of arrays have been marketed. However, none of these arrays is usable for the breeding of Triticeae species. Meanwhile, while breeding using genetic markers can greatly improve efficiency as compared with the conventional screening conducted in a field, the genotype of each genetic marker needs to be confirmed individually. In breeding, large numbers of agriculturally desirable traits are screened for and undesirable traits are selected out. If genotypes of these multiple genetic markers were confirmed comprehensively, it would be possible to further improve efficiency of breeding.
The present invention was made in view of the foregoing problems, and an object of the invention is to provide a detection instrument for detecting, in Triticeae species, gene expression, gene polymorphism, proteins (polypeptides), and substances that interact with proteins (polypeptides).